[TartanJack]

On any exhaust, it is best to work from the tip to the engine, for best flow. A well designed system reduces restriction- allowing a better/smoother exhaust flow.

Another factor to consider is "backpressure" - which helps lower-mid range. If you remove enough restriction to have very little backpressure, you'll have more top-end power but less mid-range. The trick is balancing the two . . .

 

[TartanJack]

The "S-pipe" is between the header and the "scuba tank" (cat #2 and resonator). That exhaust goes after the scuba.
So, different part of the system.

 

[TartanJack]

If it acts weird, unplug the battery, wait a bit (15 minutes or more) and replug. That should reset the ECU and it relearn the power band/curve w/ the header.